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                    <div id="header">
                <h1 class="title">This is the title of the thesis</h1>
                                <h1 class="subtitle">This is the
subtitle of the thesis</h1>
                                                <h2 class="author">Firstname
Surname</h2>
                                                <h3 class="date">January
2015</h3>
                            </div>
        
                    <div id="TOC">
                <ul>
                <li><a href="#abstract"
                id="toc-abstract">Abstract</a></li>
                <li><a href="#acknowledgements"
                id="toc-acknowledgements">Acknowledgements</a></li>
                <li><span class="toc-section-number">1</span> List of
                Figures</li>
                <li><span class="toc-section-number">2</span> List of
                Tables</li>
                <li><a href="#abbreviations"
                id="toc-abbreviations">Abbreviations</a></li>
                <li><a href="#sec:intro" id="toc-sec:intro"><span
                class="toc-section-number">3</span> Introduction, with a
                citation</a>
                <ul>
                <li><a href="#background" id="toc-background"><span
                class="toc-section-number">3.1</span>
                Background</a></li>
                <li><a href="#the-middle-bit"
                id="toc-the-middle-bit"><span
                class="toc-section-number">3.2</span> The middle bit</a>
                <ul>
                <li><a href="#subsection-of-the-middle-bit"
                id="toc-subsection-of-the-middle-bit"><span
                class="toc-section-number">3.2.1</span> Subsection of
                the middle bit</a></li>
                </ul></li>
                <li><a href="#summary-of-chapters"
                id="toc-summary-of-chapters"><span
                class="toc-section-number">3.3</span> Summary of
                chapters</a></li>
                </ul></li>
                <li><a href="#sec:lit-review"
                id="toc-sec:lit-review"><span
                class="toc-section-number">4</span> Literature review,
                with maths</a>
                <ul>
                <li><a href="#introduction" id="toc-introduction"><span
                class="toc-section-number">4.1</span>
                Introduction</a></li>
                <li><a href="#the-middle" id="toc-the-middle"><span
                class="toc-section-number">4.2</span> The
                middle</a></li>
                <li><a href="#a-complicated-math-equation"
                id="toc-a-complicated-math-equation"><span
                class="toc-section-number">4.3</span> A complicated math
                equation</a></li>
                <li><a href="#conclusion" id="toc-conclusion"><span
                class="toc-section-number">4.4</span>
                Conclusion</a></li>
                </ul></li>
                <li><a href="#sec:research-code"
                id="toc-sec:research-code"><span
                class="toc-section-number">5</span> First research
                study, with code</a>
                <ul>
                <li><a href="#introduction-1"
                id="toc-introduction-1"><span
                class="toc-section-number">5.1</span>
                Introduction</a></li>
                <li><a href="#method" id="toc-method"><span
                class="toc-section-number">5.2</span> Method</a>
                <ul>
                <li><a href="#sec:subsec-code"
                id="toc-sec:subsec-code"><span
                class="toc-section-number">5.2.1</span> Subsection 1
                with example code block</a></li>
                <li><a href="#subsection-2" id="toc-subsection-2"><span
                class="toc-section-number">5.2.2</span> Subsection
                2</a></li>
                </ul></li>
                <li><a href="#results" id="toc-results"><span
                class="toc-section-number">5.3</span> Results</a></li>
                <li><a href="#discussion" id="toc-discussion"><span
                class="toc-section-number">5.4</span>
                Discussion</a></li>
                <li><a href="#conclusion-1" id="toc-conclusion-1"><span
                class="toc-section-number">5.5</span>
                Conclusion</a></li>
                </ul></li>
                <li><a href="#sec:research-figure"
                id="toc-sec:research-figure"><span
                class="toc-section-number">6</span> Research containing
                a figure</a>
                <ul>
                <li><a href="#introduction-2"
                id="toc-introduction-2"><span
                class="toc-section-number">6.1</span>
                Introduction</a></li>
                <li><a href="#method-1" id="toc-method-1"><span
                class="toc-section-number">6.2</span> Method</a>
                <ul>
                <li><a href="#subsection-1" id="toc-subsection-1"><span
                class="toc-section-number">6.2.1</span> Subsection
                1</a></li>
                <li><a href="#subsection-2-1"
                id="toc-subsection-2-1"><span
                class="toc-section-number">6.2.2</span> Subsection
                2</a></li>
                </ul></li>
                <li><a href="#results-1" id="toc-results-1"><span
                class="toc-section-number">6.3</span> Results</a></li>
                <li><a href="#discussion-1" id="toc-discussion-1"><span
                class="toc-section-number">6.4</span>
                Discussion</a></li>
                <li><a href="#conclusion-2" id="toc-conclusion-2"><span
                class="toc-section-number">6.5</span>
                Conclusion</a></li>
                </ul></li>
                <li><a href="#sec:research-table"
                id="toc-sec:research-table"><span
                class="toc-section-number">7</span> Research containing
                a table</a>
                <ul>
                <li><a href="#introduction-3"
                id="toc-introduction-3"><span
                class="toc-section-number">7.1</span>
                Introduction</a></li>
                <li><a href="#method-2" id="toc-method-2"><span
                class="toc-section-number">7.2</span> Method</a>
                <ul>
                <li><a href="#subsection-1-1"
                id="toc-subsection-1-1"><span
                class="toc-section-number">7.2.1</span> Subsection
                1</a></li>
                <li><a href="#subsection-2-2"
                id="toc-subsection-2-2"><span
                class="toc-section-number">7.2.2</span> Subsection
                2</a></li>
                </ul></li>
                <li><a href="#results-2" id="toc-results-2"><span
                class="toc-section-number">7.3</span> Results</a></li>
                <li><a href="#discussion-2" id="toc-discussion-2"><span
                class="toc-section-number">7.4</span>
                Discussion</a></li>
                <li><a href="#conclusion-3" id="toc-conclusion-3"><span
                class="toc-section-number">7.5</span>
                Conclusion</a></li>
                </ul></li>
                <li><a href="#sec:research-final"
                id="toc-sec:research-final"><span
                class="toc-section-number">8</span> Final research
                study</a>
                <ul>
                <li><a href="#introduction-4"
                id="toc-introduction-4"><span
                class="toc-section-number">8.1</span>
                Introduction</a></li>
                <li><a href="#method-3" id="toc-method-3"><span
                class="toc-section-number">8.2</span> Method</a>
                <ul>
                <li><a href="#subsection-1-2"
                id="toc-subsection-1-2"><span
                class="toc-section-number">8.2.1</span> Subsection
                1</a></li>
                <li><a href="#subsection-2-3"
                id="toc-subsection-2-3"><span
                class="toc-section-number">8.2.2</span> Subsection
                2</a></li>
                </ul></li>
                <li><a href="#results-3" id="toc-results-3"><span
                class="toc-section-number">8.3</span> Results</a></li>
                <li><a href="#discussion-3" id="toc-discussion-3"><span
                class="toc-section-number">8.4</span>
                Discussion</a></li>
                <li><a href="#conclusion-4" id="toc-conclusion-4"><span
                class="toc-section-number">8.5</span>
                Conclusion</a></li>
                </ul></li>
                <li><a href="#sec:conclusion"
                id="toc-sec:conclusion"><span
                class="toc-section-number">9</span> Conclusion</a>
                <ul>
                <li><a href="#thesis-summary"
                id="toc-thesis-summary"><span
                class="toc-section-number">9.1</span> Thesis
                summary</a></li>
                <li><a href="#future-work" id="toc-future-work"><span
                class="toc-section-number">9.2</span> Future
                work</a></li>
                </ul></li>
                <li><a href="#appendix-1-some-extra-stuff"
                id="toc-appendix-1-some-extra-stuff">Appendix 1: Some
                extra stuff</a></li>
                <li><a href="#appendix-2-some-more-extra-stuff"
                id="toc-appendix-2-some-more-extra-stuff">Appendix 2:
                Some more extra stuff</a></li>
                <li><a href="#references"
                id="toc-references">References</a></li>
                </ul>
            </div>
                                <!-- This page is for an official declaration. -->
                                <p> </p>
                                <h1 class="unnumbered"
                                id="abstract">Abstract</h1>
                                <!-- This is the abstract -->
                                <p>Lorem ipsum dolor sit amet,
                                consectetur adipiscing elit. Nam et
                                turpis gravida, lacinia ante sit amet,
                                sollicitudin erat. Aliquam efficitur
                                vehicula leo sed condimentum. Phasellus
                                lobortis eros vitae rutrum egestas.
                                Vestibulum ante ipsum primis in faucibus
                                orci luctus et ultrices posuere cubilia
                                Curae; Donec at urna imperdiet,
                                vulputate orci eu, sollicitudin leo.
                                Donec nec dui sagittis, malesuada erat
                                eget, vulputate tellus. Nam ullamcorper
                                efficitur iaculis. Mauris eu vehicula
                                nibh. In lectus turpis, tempor at felis
                                a, egestas fermentum massa.</p>
                                <h1 class="unnumbered"
                                id="acknowledgements">Acknowledgements</h1>
                                <!-- This is for acknowledging all of the people who helped out -->
                                <p>Interdum et malesuada fames ac ante
                                ipsum primis in faucibus. Aliquam congue
                                fermentum ante, semper porta nisl
                                consectetur ut. Duis ornare sit amet dui
                                ac faucibus. Phasellus ullamcorper leo
                                vitae arcu ultricies cursus. Duis
                                tristique lacus eget metus bibendum, at
                                dapibus ante malesuada. In dictum nulla
                                nec porta varius. Fusce et elit eget
                                sapien fringilla maximus in sit amet
                                dui.</p>
                                <p>Mauris eget blandit nisi, faucibus
                                imperdiet odio. Suspendisse blandit
                                dolor sed tellus venenatis, venenatis
                                fringilla turpis pretium. Donec pharetra
                                arcu vitae euismod tincidunt. Morbi ut
                                turpis volutpat, ultrices felis non,
                                finibus justo. Proin convallis accumsan
                                sem ac vulputate. Sed rhoncus ipsum eu
                                urna placerat, sed rhoncus erat
                                facilisis. Praesent vitae vestibulum
                                dui. Proin interdum tellus ac velit
                                varius, sed finibus turpis placerat.</p>
                                <!-- Use the \newpage command to force a new page -->
                                <h1 data-number="1"><span
                                class="header-section-number">1</span>
                                List of Figures</h1>
                                <div class="list list-of-fig">
                                1. RV Calypso is a former British Royal
                                Navy minesweeper converted into a
                                research vessel for the oceanographic
                                researcher Jacques-Yves Cousteau. It was
                                equipped with a mobile laboratory for
                                underwater field research.<br />

                                2. This is not a boat<br />

                                </div>
                                <!--
                                The \listoffigures will use short captions first, and the whole caption if none is present. To keep this list readable, ensure each figure has a short caption, e.g.
                                ![main_text_caption](source/figures/my_image.pdf ){#fig:mylabel}{ width=50% short-caption="short caption"}

                                See chapter 4 for more examples.
                                -->
                                <h1 data-number="2"><span
                                class="header-section-number">2</span>
                                List of Tables</h1>
                                <div class="list list-of-tbl">

                                </div>
                                <!--
                                The \listoffigures will use short captions first, and the whole caption if none is present. To keep this list readable, ensure each figure has a short caption, e.g.

                                +----------+----------+----------+
                                |   Test   |  Test2   |  Test3   |
                                +----------+----------+----------+
                                |    20    |    22    |    23    |
                                +----------+----------+----------+
                                |    34    |    35    |    36    |
                                +----------+----------+----------+
                                :  Long caption []{#tbl:tbl_ref short-caption="short caption"}

                                You MUST include the empty square brackets before the curly brackets.

                                See chapter 5 for more examples.
                                -->
                                <h1 class="unnumbered"
                                id="abbreviations">Abbreviations</h1>

                                <h1 data-number="3" id="sec:intro"><span
                                class="header-section-number">3</span>
                                Introduction, with a citation</h1>
                                <h2 data-number="3.1"
                                id="background"><span
                                class="header-section-number">3.1</span>
                                Background</h2>
                                <p>This is the introduction. Quisque
                                finibus aliquet cursus. Integer in
                                pellentesque tellus. Duis eu dignissim
                                nulla, a porttitor enim. Quisque
                                vehicula leo non ultrices finibus. Duis
                                vehicula quis sem sit amet sollicitudin.
                                Integer neque est, pharetra et auctor
                                vel, iaculis interdum lectus.</p>
                                <!-- 
                                To include a reference, add the citation key shown in the references.bib file.
                                -->
                                <p>To include a citation to the text,
                                just add the citation key shown in the
                                references.bib file. The style of the
                                citation is determined by the
                                ref_format.csl file. For example, in The
                                Living Sea you can find pictures of the
                                Calypso <span class="citation"
                                data-cites="Cousteau1963">(Cousteau
                                Jacques &amp; Dugan James
                                1963)</span>.</p>
                                <p>In neque mauris, maximus at sapien a,
                                iaculis dignissim justo. Aliquam erat
                                volutpat. Praesent varius risus auctor
                                est ultricies, sit amet consequat nisi
                                laoreet. Suspendisse non est et mauris
                                pharetra sagittis non porta justo.
                                Praesent malesuada metus ut sapien
                                sodales ornare.</p>
                                <h2 data-number="3.2"
                                id="the-middle-bit"><span
                                class="header-section-number">3.2</span>
                                The middle bit</h2>
                                <p>This is the middle bit. Phasellus
                                quis ex in ipsum pellentesque lobortis
                                tincidunt sed massa. Nullam euismod sem
                                quis dictum condimentum. Suspendisse
                                risus metus, elementum eu congue quis,
                                viverra ac metus. Donec non lectus at
                                lectus euismod laoreet pharetra semper
                                dui. Donec sed eleifend erat, vel
                                ultrices nibh. Nam scelerisque turpis ac
                                nunc mollis, et rutrum nisl luctus.</p>
                                <p>Duis faucibus vestibulum elit, sit
                                amet lobortis libero. Class aptent
                                taciti sociosqu ad litora torquent per
                                conubia nostra, per inceptos himenaeos.
                                Sed at cursus nibh. Sed accumsan
                                imperdiet interdum. Proin id facilisis
                                tortor. Proin posuere a neque nec
                                iaculis. Suspendisse potenti. Nullam
                                hendrerit ante mi, vitae iaculis dui
                                laoreet eu.</p>
                                <p>Cras eleifend velit diam, eu viverra
                                mi volutpat ut. Cum sociis natoque
                                penatibus et magnis dis parturient
                                montes, nascetur ridiculus mus. Donec
                                finibus leo nec dui imperdiet, tincidunt
                                ornare orci venenatis. Maecenas placerat
                                efficitur est, eu blandit magna
                                hendrerit eu.</p>
                                <h3 data-number="3.2.1"
                                id="subsection-of-the-middle-bit"><span
                                class="header-section-number">3.2.1</span>
                                Subsection of the middle bit</h3>
                                <p>This is a subsection of the middle
                                bit. Quisque sit amet tempus arcu, ac
                                suscipit ante. Cras massa elit,
                                pellentesque eget nisl ut, malesuada
                                rutrum risus. Nunc in venenatis mi.
                                Curabitur sit amet suscipit eros, non
                                tincidunt nibh. Phasellus lorem lectus,
                                iaculis non luctus eget, tempus non
                                risus. Suspendisse ut felis mi.</p>
                                <h2 data-number="3.3"
                                id="summary-of-chapters"><span
                                class="header-section-number">3.3</span>
                                Summary of chapters</h2>
                                <!--
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                                For bold, add ** on either side of the text
                                For bold and italic, add _** on either side of the text
                                -->
                                <p>This is a brief outline of what went
                                into each chapter, and a section which
                                shows how to reference headers (which
                                are labelled automatically for you).
                                This chapter, Section 1, shows how to
                                use citations and how to reference
                                section headers. Section 2 shows how use
                                and reference equations. Section 3 shows
                                how to use and reference code. Section 4
                                shows how to use, reference, and resize
                                pdf and jpg figures. Section 5 shows how
                                to use and reference tables. Section 6
                                is truly revolutionary (but shows
                                nothing functional). <strong><a
                                href="#appendix-1-some-extra-stuff">Appendix
                                1</a></strong> shows how to add chapters
                                which are not numbered, and has to be
                                referenced manually, as does <strong><a
                                href="#appendix-2-some-more-extra-stuff">Appendix
                                2</a></strong>. See the base <a
                                href="https://github.com/tompollard/phd_thesis_markdown/blob/master/README.md"><code>README.md</code></a>
                                for how References are handled - leave
                                <code>*_references.md</code> alone, and
                                provide it to <code>pandoc</code>
                                last.</p>
                                <p>Proin faucibus nibh sit amet augue
                                blandit varius.</p>
                                <h1 data-number="4"
                                id="sec:lit-review"><span
                                class="header-section-number">4</span>
                                Literature review, with maths</h1>
                                <!--
                                After the introductory chapter, it seems fairly common to
                                include a chapter that reviews the literature and
                                introduces methodology used throughout the thesis.
                                -->
                                <h2 data-number="4.1"
                                id="introduction"><span
                                class="header-section-number">4.1</span>
                                Introduction</h2>
                                <p>This is the introduction. Duis in
                                neque felis. In hac habitasse platea
                                dictumst. Cras eget rutrum elit.
                                Pellentesque tristique venenatis
                                pellentesque. Cras eu dignissim quam,
                                vel sodales felis. Vestibulum efficitur
                                justo a nibh cursus eleifend. Integer
                                ultrices lorem at nunc efficitur
                                lobortis.</p>
                                <h2 data-number="4.2"
                                id="the-middle"><span
                                class="header-section-number">4.2</span>
                                The middle</h2>
                                <p>This is the literature review. Nullam
                                quam odio, volutpat ac ornare quis,
                                vestibulum nec nulla. Aenean nec dapibus
                                in mL/min<sup>-1</sup>. Mathematical
                                formula can be inserted using Latex and
                                can be automatically numbered:</p>
                                <p><span id="eq:my_equation"><span
                                class="math display"><em>f</em>(<em>x</em>) = <em>a</em><em>x</em><sup>3</sup> + <em>b</em><em>x</em><sup>2</sup> + <em>c</em><em>x</em> + <em>d</em>   (1)</span></span></p>
                                <p>Nunc eleifend, ex a luctus porttitor,
                                felis ex suscipit tellus, ut
                                sollicitudin sapien purus in libero.
                                Nulla blandit eget urna vel tempus.
                                Praesent fringilla dui sapien, sit amet
                                egestas leo sollicitudin at.</p>
                                <p>Later on in the text, you can
                                reference Equation 1 and its
                                mind-blowing ramifications. Pellentesque
                                habitant morbi tristique senectus et
                                netus et malesuada fames ac turpis
                                egestas. Sed faucibus pulvinar volutpat.
                                Ut semper fringilla erat non dapibus.
                                Nunc vitae felis eget purus placerat
                                finibus laoreet ut nibh.</p>
                                <h2 data-number="4.3"
                                id="a-complicated-math-equation"><span
                                class="header-section-number">4.3</span>
                                A complicated math equation</h2>
                                <p>The following raw text in markdown
                                behind Equation 2 shows that you can
                                fall back on if it is more convenient
                                for you. Note that this will only be
                                rendered in <code>thesis.pdf</code></p>
                                <p><span
                                id="eq:my_complicated_equation"><span
                                class="math display">$$
                                \begin{aligned}
                                    \hat{\theta}_g = \argmin_{\theta_g}
                                \Big\{ - &amp;\sum^{N}_{n=1}\Big(
                                1-\mathbb{1}[f(\pmb x^{(n)})]\Big)\log
                                f\Big(\pmb x^{(n)} \\
                                    &amp;+ g(\pmb x^{(n)};\theta_g)\Big)
                                + \lambda|g(\pmb x^{(n)};\theta_g)|_2
                                \Big\} \ ,
                                \end{aligned}
                                \qquad{(2)}$$</span></span></p>
                                <h2 data-number="4.4"
                                id="conclusion"><span
                                class="header-section-number">4.4</span>
                                Conclusion</h2>
                                <p>This is the conclusion. Donec
                                pulvinar molestie urna eu faucibus. In
                                tristique ut neque vel eleifend. Morbi
                                ut massa vitae diam gravida iaculis.
                                Pellentesque habitant morbi tristique
                                senectus et netus et malesuada fames ac
                                turpis egestas.</p>
                                <!-- Insert an unordered list -->
                                <ul>
                                <li>first item in the list</li>
                                <li>second item in the list</li>
                                <li>third item in the list</li>
                                </ul>
                                <h1 data-number="5"
                                id="sec:research-code"><span
                                class="header-section-number">5</span>
                                First research study, with code</h1>
                                <h2 data-number="5.1"
                                id="introduction-1"><span
                                class="header-section-number">5.1</span>
                                Introduction</h2>
                                <p>This is the introduction. Nam mollis
                                congue tortor, sit amet convallis tortor
                                mollis eget. Fusce viverra ut magna eu
                                sagittis. Vestibulum at ultrices sapien,
                                at elementum urna. Nam a blandit leo,
                                non lobortis quam. Aliquam feugiat
                                turpis vitae tincidunt ultricies. Mauris
                                ullamcorper pellentesque nisl, vel
                                molestie lorem viverra at.</p>
                                <h2 data-number="5.2" id="method"><span
                                class="header-section-number">5.2</span>
                                Method</h2>
                                <p>Suspendisse iaculis in lacus ut
                                dignissim. Cras dignissim dictum
                                eleifend. Suspendisse potenti.
                                Suspendisse et nisi suscipit, vestibulum
                                est at, maximus sapien. Sed ut diam
                                tortor.</p>
                                <h3 data-number="5.2.1"
                                id="sec:subsec-code"><span
                                class="header-section-number">5.2.1</span>
                                Subsection 1 with example code
                                block</h3>
                                <p>This is the first part of the
                                methodology. Cras porta dui a dolor
                                tincidunt placerat. Cras scelerisque sem
                                et malesuada vestibulum. Vivamus
                                faucibus ligula ac sodales consectetur.
                                Aliquam vel tristique nisl. Aliquam erat
                                volutpat. Pellentesque iaculis enim sit
                                amet posuere facilisis. Integer egestas
                                quam sit amet nunc maximus, id bibendum
                                ex blandit.</p>
                                <p>For syntax highlighting in code
                                blocks, add three “`” characters before
                                and after a code block:</p>
                                <div id="lst:code"
                                class="listing python">
                                <p>Listing 1: Code caption</p>
                                <div class="sourceCode" id="cb1"><pre
                                class="sourceCode python"><code class="sourceCode python"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a>mood <span class="op">=</span> <span class="st">&#39;happy&#39;</span></span>
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="cf">if</span> mood <span class="op">==</span> <span class="st">&#39;happy&#39;</span>:</span>
<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a>    <span class="bu">print</span>(<span class="st">&quot;I am a happy robot&quot;</span>)</span></code></pre></div>
                                </div>
                                <p>You can then reference the code block
                                like this (Listing 1).</p>
                                <h3 data-number="5.2.2"
                                id="subsection-2"><span
                                class="header-section-number">5.2.2</span>
                                Subsection 2</h3>
                                <p>By running the code in Section 3.2.1,
                                we solved AI completely. This is the
                                second part of the methodology. Proin
                                tincidunt odio non sem mollis tristique.
                                Fusce pharetra accumsan volutpat. In nec
                                mauris vel orci rutrum dapibus nec ac
                                nibh. Praesent malesuada sagittis nulla,
                                eget commodo mauris ultricies eget.
                                Suspendisse iaculis finibus ligula.</p>
                                <!-- 
                                Comments can be added like this.
                                -->
                                <h2 data-number="5.3" id="results"><span
                                class="header-section-number">5.3</span>
                                Results</h2>
                                <p>These are the results. Ut accumsan
                                tempus aliquam. Sed massa ex, egestas
                                non libero id, imperdiet scelerisque
                                augue. Duis rutrum ultrices arcu et
                                ultricies. Proin vel elit eu magna
                                mattis vehicula. Sed ex erat, fringilla
                                vel feugiat ut, fringilla non diam.</p>
                                <h2 data-number="5.4"
                                id="discussion"><span
                                class="header-section-number">5.4</span>
                                Discussion</h2>
                                <p>This is the discussion. Duis ultrices
                                tempor sem vitae convallis. Pellentesque
                                lobortis risus ac nisi varius bibendum.
                                Phasellus volutpat aliquam varius.
                                Mauris vitae neque quis libero volutpat
                                finibus. Nunc diam metus, imperdiet
                                vitae leo sed, varius posuere orci.</p>
                                <h2 data-number="5.5"
                                id="conclusion-1"><span
                                class="header-section-number">5.5</span>
                                Conclusion</h2>
                                <p>This is the conclusion to the
                                chapter. Praesent bibendum urna orci, a
                                venenatis tellus venenatis at. Etiam
                                ornare, est sed lacinia elementum,
                                lectus diam tempor leo, sit amet
                                elementum ex elit id ex. Ut ac viverra
                                turpis. Quisque in nisl auctor, ornare
                                dui ac, consequat tellus.</p>
                                <h1 data-number="6"
                                id="sec:research-figure"><span
                                class="header-section-number">6</span>
                                Research containing a figure</h1>
                                <h2 data-number="6.1"
                                id="introduction-2"><span
                                class="header-section-number">6.1</span>
                                Introduction</h2>
                                <p>This is the introduction. Sed
                                vulputate tortor at nisl blandit
                                interdum. Cras sagittis massa ex, quis
                                eleifend purus condimentum congue.
                                Maecenas tristique, justo vitae
                                efficitur mollis, mi nulla varius elit,
                                in consequat ligula nulla ut augue.
                                Phasellus diam sapien, placerat sit amet
                                tempor non, lobortis tempus ante.</p>
                                <h2 data-number="6.2"
                                id="method-1"><span
                                class="header-section-number">6.2</span>
                                Method</h2>
                                <p>Donec imperdiet, lectus vestibulum
                                sagittis tempus, turpis dolor euismod
                                justo, vel tempus neque libero sit amet
                                tortor. Nam cursus commodo
                                tincidunt.</p>
                                <h3 data-number="6.2.1"
                                id="subsection-1"><span
                                class="header-section-number">6.2.1</span>
                                Subsection 1</h3>
                                <p>This is the first part of the
                                methodology. Duis tempor sapien sed
                                tellus ultrices blandit. Sed porta
                                mauris tortor, eu vulputate arcu dapibus
                                ac. Curabitur sodales at felis efficitur
                                sollicitudin. Quisque at neque
                                sollicitudin, mollis arcu vitae,
                                faucibus tellus.</p>
                                <h3 data-number="6.2.2"
                                id="subsection-2-1"><span
                                class="header-section-number">6.2.2</span>
                                Subsection 2</h3>
                                <p>This is the second part of the
                                methodology. Sed ut ipsum ultrices,
                                interdum ipsum vel, lobortis diam.
                                Curabitur sit amet massa quis tortor
                                molestie dapibus a at libero. Mauris
                                mollis magna quis ante vulputate
                                consequat. Integer leo turpis, suscipit
                                ac venenatis pellentesque, efficitur non
                                sem. Pellentesque eget vulputate turpis.
                                Etiam id nibh at elit fermentum
                                interdum.</p>
                                <!-- 
                                Comments can be added like this.
                                -->
                                <h2 data-number="6.3"
                                id="results-1"><span
                                class="header-section-number">6.3</span>
                                Results</h2>
                                <p>These are the results. In vitae odio
                                at libero elementum fermentum vel
                                iaculis enim. Nullam finibus sapien in
                                congue condimentum. Curabitur et ligula
                                et ipsum mollis fringilla.</p>
                                <h2 data-number="6.4"
                                id="discussion-1"><span
                                class="header-section-number">6.4</span>
                                Discussion</h2>
                                <!--
                                Figures can be either referenced using @fig:mylabel. See https://lierdakil.github.io/pandoc-crossref/
                                -->
                                <p>Figure 1 shows how to add a figure.
                                Donec ut lacinia nibh. Nam tincidunt
                                augue et tristique cursus. Vestibulum
                                sagittis odio nisl, a malesuada turpis
                                blandit quis. Cras ultrices metus tempor
                                laoreet sodales. Nam molestie ipsum ac
                                imperdiet laoreet. Pellentesque habitant
                                morbi tristique senectus et netus et
                                malesuada fames ac turpis egestas.</p>
                                <!-- 
                                Figures can be added with the following syntax:
                                ![main_text_caption](source/figures/my_image.pdf ){#fig:mylabel width=50% short-caption="short caption"}

                                For details on setting attributes like width and height, see:
                                http://pandoc.org/MANUAL.html#extension-link_attributes
                                -->
                                <figure id="fig:my_fig">
                                <embed
                                src="source/figures/example_figure.pdf"
                                style="width:100.0%"
                                data-short-caption="Figure short caption" />
                                <figcaption>Figure 1: RV Calypso is a
                                former British Royal Navy minesweeper
                                converted into a research vessel for the
                                oceanographic researcher Jacques-Yves
                                Cousteau. It was equipped with a mobile
                                laboratory for underwater field
                                research.</figcaption>
                                </figure>
                                <h2 data-number="6.5"
                                id="conclusion-2"><span
                                class="header-section-number">6.5</span>
                                Conclusion</h2>
                                <p>This is the conclusion to the
                                chapter. Quisque nec purus a quam
                                consectetur volutpat. Cum sociis natoque
                                penatibus et magnis dis parturient
                                montes, nascetur ridiculus mus. In lorem
                                justo, convallis quis lacinia eget,
                                laoreet eu metus. Fusce blandit tellus
                                tellus. Curabitur nec cursus odio.
                                Quisque tristique eros nulla, vitae
                                finibus lorem aliquam quis. Interdum et
                                malesuada fames ac ante ipsum primis in
                                faucibus.</p>
                                <!--
                                Below is an example that does not utilize the shortcaption feature, as it already fits neatly on a line. Note that multiple file formats are acceptable for sources (jpg, tiff, pdf, etc.)
                                -->
                                <figure id="fig:other_fig">
                                <img
                                src="source/figures/full_caption_example.jpg"
                                style="width:100.0%"
                                alt="This is not a boat" />
                                <figcaption>Figure 2: This is not a
                                boat</figcaption>
                                </figure>
                                <h1 data-number="7"
                                id="sec:research-table"><span
                                class="header-section-number">7</span>
                                Research containing a table</h1>
                                <h2 data-number="7.1"
                                id="introduction-3"><span
                                class="header-section-number">7.1</span>
                                Introduction</h2>
                                <p>This is the introduction. Phasellus
                                non purus id mauris aliquam rutrum vitae
                                quis tellus. Maecenas rhoncus ligula
                                nulla, fringilla placerat mi consectetur
                                eu. Aenean nec metus ac est ornare
                                posuere. Nunc ipsum lacus, gravida
                                commodo turpis quis, rutrum eleifend
                                erat. Pellentesque id lorem eget ante
                                porta tincidunt nec nec tellus.</p>
                                <h2 data-number="7.2"
                                id="method-2"><span
                                class="header-section-number">7.2</span>
                                Method</h2>
                                <p>Vivamus consectetur, velit in congue
                                lobortis, massa massa lacinia urna,
                                sollicitudin semper ipsum augue quis
                                tortor. Donec quis nisl at arcu volutpat
                                ultrices. Maecenas ex nibh, consequat ac
                                blandit sit amet, molestie in odio.
                                Morbi finibus libero et nisl dignissim,
                                at ultricies ligula pulvinar.</p>
                                <h3 data-number="7.2.1"
                                id="subsection-1-1"><span
                                class="header-section-number">7.2.1</span>
                                Subsection 1</h3>
                                <p>This is the first part of the
                                methodology. Integer leo erat, commodo
                                in lacus vel, egestas varius elit. Nulla
                                eget magna quam. Nullam sollicitudin
                                dolor ut ipsum varius tincidunt. Duis
                                dignissim massa in ipsum accumsan
                                imperdiet. Maecenas suscipit sapien sed
                                dui pharetra blandit. Morbi fermentum
                                est vel quam pretium maximus.</p>
                                <h3 data-number="7.2.2"
                                id="subsection-2-2"><span
                                class="header-section-number">7.2.2</span>
                                Subsection 2</h3>
                                <p>This is the second part of the
                                methodology. Nullam accumsan condimentum
                                eros eu volutpat. Maecenas quis ligula
                                tempor, interdum ante sit amet, aliquet
                                sem. Fusce tellus massa, blandit id
                                tempus at, cursus in tortor. Nunc nec
                                volutpat ante. Phasellus dignissim ut
                                lectus quis porta. Lorem ipsum dolor sit
                                amet, consectetur adipiscing elit.</p>
                                <!-- 
                                Comments can be added like this.
                                -->
                                <h2 data-number="7.3"
                                id="results-2"><span
                                class="header-section-number">7.3</span>
                                Results</h2>
                                <!-- Table formatting works same as figure formatting -->
                                <p>Table <strong>¿tbl:random?</strong>
                                shows us how to add a table. Integer
                                tincidunt sed nisl eget pellentesque.
                                Mauris eleifend, nisl non lobortis
                                fringilla, sapien eros aliquet orci,
                                vitae pretium massa neque eu turpis.
                                Pellentesque tincidunt aliquet volutpat.
                                Ut ornare dui id ex sodales laoreet.</p>
                                <!-- Force the table onto a newpage -->
                                <table>
                                <caption>Important data for various land
                                masses. <span id="tbl:random"
                                data-short-caption="Table short caption"></span></caption>
                                <colgroup>
                                <col style="width: 15%" />
                                <col style="width: 9%" />
                                <col style="width: 11%" />
                                <col style="width: 17%" />
                                <col style="width: 15%" />
                                <col style="width: 15%" />
                                <col style="width: 15%" />
                                </colgroup>
                                <thead>
                                <tr class="header">
                                <th
                                style="text-align: left;">Landmass</th>
                                <th style="text-align: center;">%
                                stuff</th>
                                <th style="text-align: center;">Number
                                of Owls</th>
                                <th style="text-align: center;">Dolphins
                                per Capita</th>
                                <th style="text-align: center;">How Many
                                Foos</th>
                                <th style="text-align: center;">How Many
                                Bars</th>
                                <th
                                style="text-align: center;">Forbidden
                                Float</th>
                                </tr>
                                </thead>
                                <tbody>
                                <tr class="odd">
                                <td style="text-align: left;">North
                                America</td>
                                <td style="text-align: center;">94%</td>
                                <td
                                style="text-align: center;">20,028</td>
                                <td
                                style="text-align: center;">17,465</td>
                                <td
                                style="text-align: center;">12,084</td>
                                <td
                                style="text-align: center;">20,659</td>
                                <td
                                style="text-align: center;">1.71</td>
                                </tr>
                                <tr class="even">
                                <td style="text-align: left;">Central
                                America</td>
                                <td style="text-align: center;">91%</td>
                                <td
                                style="text-align: center;">6564</td>
                                <td
                                style="text-align: center;">6350</td>
                                <td
                                style="text-align: center;">8,189</td>
                                <td
                                style="text-align: center;">12,012</td>
                                <td
                                style="text-align: center;">1.52</td>
                                </tr>
                                <tr class="odd">
                                <td style="text-align: left;">South
                                America</td>
                                <td style="text-align: center;">86%</td>
                                <td
                                style="text-align: center;">3902</td>
                                <td
                                style="text-align: center;">4127</td>
                                <td
                                style="text-align: center;">5,205</td>
                                <td
                                style="text-align: center;">6,565</td>
                                <td
                                style="text-align: center;">1.28</td>
                                </tr>
                                <tr class="even">
                                <td
                                style="text-align: left;">Africa</td>
                                <td style="text-align: center;">84%</td>
                                <td
                                style="text-align: center;">2892</td>
                                <td
                                style="text-align: center;">3175</td>
                                <td
                                style="text-align: center;">3,862</td>
                                <td
                                style="text-align: center;">4,248</td>
                                <td style="text-align: center;">1.1</td>
                                </tr>
                                <tr class="odd">
                                <td
                                style="text-align: left;">Europe</td>
                                <td style="text-align: center;">92%</td>
                                <td
                                style="text-align: center;">20,964</td>
                                <td
                                style="text-align: center;">17,465</td>
                                <td
                                style="text-align: center;">15,303</td>
                                <td
                                style="text-align: center;">24,203</td>
                                <td
                                style="text-align: center;">1.58</td>
                                </tr>
                                <tr class="even">
                                <td style="text-align: left;">Asia</td>
                                <td style="text-align: center;">87%</td>
                                <td
                                style="text-align: center;">6852</td>
                                <td
                                style="text-align: center;">6350</td>
                                <td
                                style="text-align: center;">8,255</td>
                                <td
                                style="text-align: center;">11,688</td>
                                <td
                                style="text-align: center;">1.47</td>
                                </tr>
                                <tr class="odd">
                                <td
                                style="text-align: left;">Oceania</td>
                                <td style="text-align: center;">87%</td>
                                <td
                                style="text-align: center;">4044</td>
                                <td
                                style="text-align: center;">4127</td>
                                <td
                                style="text-align: center;">5,540</td>
                                <td
                                style="text-align: center;">6,972</td>
                                <td
                                style="text-align: center;">1.28</td>
                                </tr>
                                <tr class="even">
                                <td
                                style="text-align: left;">Antarctica</td>
                                <td style="text-align: center;">83%</td>
                                <td
                                style="text-align: center;">2964</td>
                                <td
                                style="text-align: center;">3175</td>
                                <td
                                style="text-align: center;">4,402</td>
                                <td
                                style="text-align: center;">4,941</td>
                                <td
                                style="text-align: center;">1.13</td>
                                </tr>
                                </tbody>
                                </table>
                                <h2 data-number="7.4"
                                id="discussion-2"><span
                                class="header-section-number">7.4</span>
                                Discussion</h2>
                                <p>This is the discussion. As we saw in
                                Table <strong>¿tbl:random?</strong>,
                                many things are true, and other things
                                are not. Etiam sit amet mi eros. Donec
                                vel nisi sed purus gravida fermentum at
                                quis odio. Vestibulum quis nisl sit amet
                                justo maximus molestie. Maecenas vitae
                                arcu erat. Nulla facilisi. Nam pretium
                                mauris eu enim porttitor, a mattis velit
                                dictum. Nulla sit amet ligula non mauris
                                volutpat fermentum quis vitae
                                sapien.</p>
                                <h2 data-number="7.5"
                                id="conclusion-3"><span
                                class="header-section-number">7.5</span>
                                Conclusion</h2>
                                <p>This is the conclusion to the
                                chapter. Nullam porta tortor id vehicula
                                interdum. Quisque pharetra, neque ut
                                accumsan suscipit, orci orci commodo
                                tortor, ac finibus est turpis eget
                                justo. Cras sodales nibh nec mauris
                                laoreet iaculis. Morbi volutpat orci
                                felis, id condimentum nulla suscipit eu.
                                Fusce in turpis quis ligula tempus
                                scelerisque eget quis odio. Vestibulum
                                et dolor id erat lobortis ullamcorper
                                quis at sem.</p>
                                <h1 data-number="8"
                                id="sec:research-final"><span
                                class="header-section-number">8</span>
                                Final research study</h1>
                                <h2 data-number="8.1"
                                id="introduction-4"><span
                                class="header-section-number">8.1</span>
                                Introduction</h2>
                                <p>This is the introduction. Nunc lorem
                                odio, laoreet eu turpis at, condimentum
                                sagittis diam. Phasellus metus ligula,
                                auctor ac nunc vel, molestie mattis
                                libero. Praesent id posuere ex, vel
                                efficitur nibh. Quisque vestibulum
                                accumsan lacus vitae mattis.</p>
                                <h2 data-number="8.2"
                                id="method-3"><span
                                class="header-section-number">8.2</span>
                                Method</h2>
                                <p>In tincidunt viverra dolor, ac
                                pharetra tellus faucibus eget.
                                Pellentesque tempor a enim nec
                                venenatis. Morbi blandit magna imperdiet
                                posuere auctor. Maecenas in maximus
                                est.</p>
                                <h3 data-number="8.2.1"
                                id="subsection-1-2"><span
                                class="header-section-number">8.2.1</span>
                                Subsection 1</h3>
                                <p>This is the first part of the
                                methodology. Praesent mollis sem diam,
                                sit amet tristique lacus vulputate quis.
                                Vivamus rhoncus est rhoncus tellus
                                lacinia, a interdum sem egestas.
                                Curabitur quis urna vel quam blandit
                                semper vitae a leo. Nam vel lectus
                                lectus.</p>
                                <h3 data-number="8.2.2"
                                id="subsection-2-3"><span
                                class="header-section-number">8.2.2</span>
                                Subsection 2</h3>
                                <p>This is the second part of the
                                methodology. Aenean vel pretium tortor.
                                Aliquam erat volutpat. Quisque quis
                                lobortis mi. Nulla turpis leo, ultrices
                                nec nulla non, ullamcorper laoreet
                                risus.</p>
                                <!-- 
                                Comments can be added like this.
                                -->
                                <h2 data-number="8.3"
                                id="results-3"><span
                                class="header-section-number">8.3</span>
                                Results</h2>
                                <p>These are the results. Curabitur
                                vulputate nisl non ante tincidunt
                                tempor. Aenean porta nisi quam, sed
                                ornare urna congue sed. Curabitur in
                                sapien justo. Quisque pulvinar
                                ullamcorper metus, eu varius mauris
                                pellentesque et. In hac habitasse platea
                                dictumst. Pellentesque nec porttitor
                                libero. Duis et magna a massa lacinia
                                cursus.</p>
                                <h2 data-number="8.4"
                                id="discussion-3"><span
                                class="header-section-number">8.4</span>
                                Discussion</h2>
                                <p>This is the discussion. Curabitur
                                gravida nisl id gravida congue. Duis est
                                nisi, sagittis eget accumsan
                                ullamcorper, semper quis turpis. Mauris
                                ultricies diam metus, sollicitudin
                                ultricies turpis lobortis vitae. Ut
                                egestas vehicula enim, porta molestie
                                neque consectetur placerat. Integer
                                iaculis sapien dolor, non porta nibh
                                condimentum ut.</p>
                                <h2 data-number="8.5"
                                id="conclusion-4"><span
                                class="header-section-number">8.5</span>
                                Conclusion</h2>
                                <p>This is the conclusion to the
                                chapter. Nulla sed condimentum lectus.
                                Duis sed tempor erat, at cursus lacus.
                                Nam vitae tempus arcu, id vestibulum
                                sapien. Cum sociis natoque penatibus et
                                magnis dis parturient montes, nascetur
                                ridiculus mus.</p>
                                <h1 data-number="9"
                                id="sec:conclusion"><span
                                class="header-section-number">9</span>
                                Conclusion</h1>
                                <!-- 
                                A chapter that concludes the thesis by summarising the learning points
                                and outlining future areas for research
                                -->
                                <h2 data-number="9.1"
                                id="thesis-summary"><span
                                class="header-section-number">9.1</span>
                                Thesis summary</h2>
                                <p>In summary, pellentesque habitant
                                morbi tristique senectus et netus et
                                malesuada fames ac turpis egestas. Nunc
                                eleifend, ex a luctus porttitor, felis
                                ex suscipit tellus, ut sollicitudin
                                sapien purus in libero. Nulla blandit
                                eget urna vel tempus. Praesent fringilla
                                dui sapien, sit amet egestas leo
                                sollicitudin at.</p>
                                <h2 data-number="9.2"
                                id="future-work"><span
                                class="header-section-number">9.2</span>
                                Future work</h2>
                                <p>There are several potential
                                directions for extending this thesis.
                                Lorem ipsum dolor sit amet, consectetur
                                adipiscing elit. Aliquam gravida ipsum
                                at tempor tincidunt. Aliquam ligula
                                nisl, blandit et dui eu, eleifend tempus
                                nibh. Nullam eleifend sapien eget ante
                                hendrerit commodo. Pellentesque pharetra
                                erat sit amet dapibus scelerisque.</p>
                                <p>Vestibulum suscipit tellus risus,
                                faucibus vulputate orci lobortis eget.
                                Nunc varius sem nisi. Nunc tempor magna
                                sapien, euismod blandit elit pharetra
                                sed. In dapibus magna convallis lectus
                                sodales, a consequat sem euismod.
                                Curabitur in interdum purus. Integer
                                ultrices laoreet aliquet. Nulla vel
                                dapibus urna. Nunc efficitur erat ac
                                nisi auctor sodales.</p>
                                <h1 class="unnumbered"
                                id="appendix-1-some-extra-stuff">Appendix
                                1: Some extra stuff</h1>
                                <!-- 
                                This could be a list of papers by the author for example 
                                -->
                                <p>Add appendix 1 here. Vivamus
                                hendrerit rhoncus interdum. Sed
                                ullamcorper et augue at porta.
                                Suspendisse facilisis imperdiet urna, eu
                                pellentesque purus suscipit in. Integer
                                dignissim mattis ex aliquam blandit.
                                Curabitur lobortis quam varius turpis
                                ultrices egestas.</p>
                                <h1 class="unnumbered"
                                id="appendix-2-some-more-extra-stuff">Appendix
                                2: Some more extra stuff</h1>
                                <!-- 
                                This could include extra figures or raw data
                                -->
                                <p>Add appendix 2 here. Aliquam rhoncus
                                mauris ac neque imperdiet, in mattis
                                eros aliquam. Etiam sed massa et risus
                                posuere rutrum vel et mauris. Integer id
                                mauris sed arcu venenatis finibus. Etiam
                                nec hendrerit purus, sed cursus nunc.
                                Pellentesque ac luctus magna. Aenean non
                                posuere enim, nec hendrerit lacus. Etiam
                                lacinia facilisis tempor. Aenean dictum
                                nunc id felis rhoncus aliquam.</p>
                                <!-- 
                                Do not edit this page.

                                References are automatically generated from the BibTex file (References.bib)

                                ...which you should create using your reference manager.
                                -->
                                <h1 class="unnumbered"
                                id="references">References</h1>
                                <div id="refs"
                                class="references csl-bib-body hanging-indent"
                                role="list">
                                <div id="ref-Cousteau1963"
                                class="csl-entry" role="listitem">
                                Cousteau Jacques &amp; Dugan James,
                                1963. <em><span class="nocase">The
                                Living Sea: by Jacques-Yves
                                Cousteau</span></em>, London: Hamish
                                Hamilton.
                                </div>
                                </div>
            </body>
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